Abstract: The removal efficiency of five different structures of quaternary ammonium salt surfactants for the Microcystis aeruginosa(MA) was studied. The comparison showed that the removal efficiency of the MA with the Gemini structure surfactant was higher than that of the common single chain surfactant, with high removal efficiency by long-chain alkanes. Using 16-6-16 as quaternary ammonium salt Gemini surfactant for study, the effects of the dosage of 16-6-16, concentration of MA solution, pH and ionic strength on removal efficiency of MA were discussed. The results showed that the removal efficiency of MA increased with the dosage of the Gemini surfactant. At high optical density (A_683nm) of 0.402,only 5 mg/L of 16-6-16 could destroy the integrity of cells，causing the cells to die consequently. As the dosage of 16-6-16 increased to 20mg/L, the removal efficiency of MA could reach above 90% after 24 h. When the dosage of 16-6-16 was 20 mg/L, the removal efficiency increased with MA solution concentration, which could achieve the highest at the A_683nm of 0.402. The removal efficiency of MA decreased with the increase of ionic strength, and the optimum pH was 7 to 9. At last, according to the study of the microscopic structure and the Zeta potential of MA solution, the mechanism of the quaternary ammonium salt Gemini surfactant for MA removal was primarily discussed.